3V9P

Crystal structure of Thymidylate kinase from Burkholderia thailandensis

PDB DOI: https://doi.org/10.2210/pdb3V9P/pdb

Classification: TRANSFERASE
Organism(s): Burkholderia thailandensis E264
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-12-27 Released: 2012-01-25
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.217
R-Value Work: 0.181
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Combining functional and structural genomics to sample the essential Burkholderia structome.

Baugh, L., Gallagher, L.A., Patrapuvich, R., Clifton, M.C., Gardberg, A.S., Edwards, T.E., Armour, B., Begley, D.W., Dieterich, S.H., Dranow, D.M., Abendroth, J., Fairman, J.W., Fox, D., Staker, B.L., Phan, I., Gillespie, A., Choi, R., Nakazawa-Hewitt, S., Nguyen, M.T., Napuli, A., Barrett, L., Buchko, G.W., Stacy, R., Myler, P.J., Stewart, L.J., Manoil, C., Van Voorhis, W.C.

(2013) PLoS One 8: e53851-e53851

PubMed: 23382856 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0053851
Primary Citation of Related Structures:
3D63, 3DAH, 3EIZ, 3EJ2, 3EK2, 3EZO, 3F0F, 3FTP, 3GK0, 3GK3, 3GVF, 3GWA, 3GWE, 3IML, 3SZ8, 3T4C, 3TML, 3TMQ, 3TXY, 3U7J, 3UE9, 3UK1, 3UK2, 3UND, 3UPT, 3URR, 3UW1, 3UW2, 3UW3, 3V2I, 3V7N, 3V8H, 3V9O, 3V9P, 3VAV, 4DDO, 4DFE, 4DHE, 4DHK, 4DUT, 4DZ4, 4E4T, 4EFI, 4EG0, 4EGJ, 4EK2, 4EQY, 4EWG, 4EXQ, 4F2G

PubMed Abstract:
The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite.

Organizational Affiliation

Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America.

Macromolecule Content

Total Structure Weight: 51.46 kDa
Atom Count: 3,452
Modelled Residue Count: 401
Deposited Residue Count: 454
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B	227	Burkholderia thailandensis E264	Mutation(s): 0 Gene Names: BTH_I2154, tmk, YP_442675.1 EC: 2.7.4.9
UniProt
Find proteins for Q2SWM4 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2SWM4 Go to UniProtKB: Q2SWM4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2SWM4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A]	C [auth A], G [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B]	F [auth A], H [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.217
R-Value Work: 0.181
R-Value Observed: 0.183
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M33V9P

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.13	α = 90
b = 77.97	β = 90
c = 84.13	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-01-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2012-01-25
Type: Initial release
Version 1.1: 2013-10-09
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3V9P

Crystal structure of Thymidylate kinase from Burkholderia thailandensis

Combining functional and structural genomics to sample the essential Burkholderia structome.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)